MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

Transposable elements are powerful mutagens. Along with genomic sequences, knock-out phenotypes and expression patterns are important information to elucidate the function of genes. In this review, I propose a strategy to develop tranposant lines on a large scale by combining genetic cross and tissue culture of Ac and Ds lines. Based on the facts that Ds tends to be inactive in F2 or later generation and Ds becomes reactivated via tissue culture, a large scale of transposants can be produced by tissue culture of seeds carrying Ac and inactive Ds. In this review, I describe limitations and considerations in operating transposon tagging systems in rice. Also, I discuss the efficiency of our gene trap system and technical procedures to clone Ds flanking DNA.

Download Full-text

Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin

10.1101/2021.07.31.454434 ◽

2021 ◽

Author(s):

Jaemyung Choi ◽

David Bruce Lyons ◽

Daniel Zilberman

Keyword(s):

Dna Methylation ◽

Transposable Elements ◽

Small Rna ◽

Histone H3 ◽

Histone H1 ◽

Dna Methyltransferases ◽

Flowering Plants ◽

Genomic Sequences ◽

Rna Molecules ◽

Rna Biogenesis

Flowering plants utilize small RNA molecules to guide DNA methyltransferases to genomic sequences. This RNA-directed DNA methylation (RdDM) pathway preferentially targets euchromatic transposable elements. However, RdDM is thought to be recruited by methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin. How RdDM is targeted to euchromatin despite an affinity for H3K9me is unclear. Here we show that loss of histone H1 enhances heterochromatic RdDM, preferentially at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation. Instead, we find that non-CG methylation is specifically required for small RNA biogenesis, and without H1 small RNA production quantitatively expands to non-CG methylated loci. Our results demonstrate that H1 enforces the separation of euchromatic and heterochromatic DNA methylation pathways by excluding the small RNA-generating branch of RdDM from non-CG methylated heterochromatin.

Download Full-text

Software Evaluation for de novo Detection of Transposons

10.1101/2021.02.08.430290 ◽

2021 ◽

Author(s):

Matias Rodriguez ◽

Wojciech Makałowski

Keyword(s):

Transposable Elements ◽

Genome Evolution ◽

De Novo ◽

Simulated Data ◽

Genomic Sequences ◽

Software Evaluation ◽

Easy Task ◽

Eukaryotic Genomes

AbstractTransposable elements (TEs) are major genomic components in most eukaryotic genomes and play an important role in genome evolution. However, despite their relevance the identification of TEs is not an easy task and a number of tools were developed to tackle this problem. To better understand how they perform, we tested several widely used tools for de novo TE detection and compared their performance on both simulated data and well curated genomic sequences. The results will be helpful for identifying common issues associated with TE-annotation and for evaluating how comparable are the results obtained with different tools.

Download Full-text

Marker utility of miniature inverted-repeat transposable elements for wheat biodiversity and evolution

Theoretical and Applied Genetics ◽

10.1007/s00122-012-1793-y ◽

2012 ◽

Vol 124 (7) ◽

pp. 1365-1373 ◽

Cited By ~ 22

Author(s):

Beery Yaakov ◽

Elif Ceylan ◽

Katherine Domb ◽

Khalil Kashkush

Keyword(s):

Transposable Elements ◽

Inverted Repeat

Download Full-text

Multigenome analysis implicates miniature inverted-repeat transposable elements (MITEs) in metabolic diversification in eudicots

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1721318115 ◽

2018 ◽

Vol 115 (28) ◽

pp. E6650-E6658 ◽

Cited By ~ 12

Author(s):

Alexander M. Boutanaev ◽

Anne E. Osbourn

Keyword(s):

Transposable Elements ◽

Inverted Repeat ◽

Cluster Formation ◽

Gene Clusters ◽

Biosynthetic Gene Cluster ◽

Terpene Synthase ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Systematic Analysis ◽

Plant Genomes

Plants produce a plethora of natural products, including many drugs. It has recently emerged that the genes encoding different natural product pathways may be organized as biosynthetic gene clusters in plant genomes, with >30 examples reported so far. Despite superficial similarities with microbes, these clusters have not arisen by horizontal gene transfer, but rather by gene duplication, neofunctionalization, and relocation via unknown mechanisms. Previously we reported that two Arabidopsis thaliana biosynthetic gene clusters are located in regions of the genome that are significantly enriched in transposable elements (TEs). Other plant biosynthetic gene clusters also harbor abundant TEs. TEs can mediate genomic rearrangement by providing homologous sequences that enable illegitimate recombination and gene relocation. Thus, TE-mediated recombination may contribute to plant biosynthetic gene cluster formation. TEs may also facilitate establishment of regulons. However, a systematic analysis of the TEs associated with plant biosynthetic gene clusters has not been carried out. Here we investigate the TEs associated with clustered terpene biosynthetic genes in multiple plant genomes and find evidence to suggest a role for miniature inverted-repeat transposable elements in cluster formation in eudicots. Through investigation of the newly sequenced Amborella trichopoda, Aquilegia coerulea, and Kalanchoe fedtschenkoi genomes, we further show that the “block” mechanism of founding of biosynthetic gene clusters through duplication and diversification of pairs of terpene synthase and cytochrome P450 genes that is prevalent in the eudicots arose around 90–130 million years ago, after the appearance of the basal eudicots and before the emergence of the superrosid clade.

Download Full-text

Sequence Organization and Conservation in sh2/a1-Homologous Regions of Sorghum and Rice

Genetics ◽

10.1093/genetics/148.1.435 ◽

1998 ◽

Vol 148 (1) ◽

pp. 435-443

Author(s):

Mingsheng Chen ◽

Phillip SanMiguel ◽

Jeffrey L Bennetzen

Keyword(s):

Transposable Elements ◽

Long Terminal Repeat ◽

Inverted Repeat ◽

Tandem Duplication ◽

Regulatory Gene ◽

Terminal Repeat ◽

Homologous Segment ◽

Sequence Organization ◽

Transcriptional Regulatory ◽

Evolutionarily Conserved

Abstract Previously, we have demonstrated microcolinearity of gene composition and orientation in sh2/a1-homologous regions of the rice, sorghum, and maize genomes. However, the sh2 and a1 homologues are only about 20 kb apart in both rice and sorghum, while they are separated by about 140 kb in maize. In order to further define sequence organization and conservation in sh2/a1-homologous regions, we have completely sequenced a 42,446-bp segment of sorghum DNA. Four genes were identified: a homologue of sh2, two homologues of a1, and a putative transcriptional regulatory gene. A solo long terminal repeat of the retroelement Leviathan was detected between the two a1 homologues, and eight miniature inverted repeat transposable elements were found in this region. Comparison of the sorghum sequence with the sequence of the homologous segment from rice indicated that only the identified genes were evolutionarily conserved between these two species, which have evolved independently for over 50 million years. The introns of the a1 homologues have evolved faster than the introns of the sh2 homologue. The a1 tandem duplication appears to be an ancient event that may have preceded the ancestral divergence of maize, sorghum, and rice.

Download Full-text